// Get the path of the configuration file
$fname = JPATH_CONFIGURATION.DS.'configuration.PHP';
// clear cache
$cache = JFactory::getCache();
$cache->clean();
// Update the credentials with the new settings
$config =& JFactory::getConfig();
$config->setValue('config.custom_var','xxx');
// Get the config registry in PHP class format and write it to configuation.PHP
jimport('joomla.filesystem.file');
if (!JFile::write($fname,$config->toString('PHP','config',array('class' => 'JConfig')))) {
die(JText::_('ERRORCONFIGFILE'));
}

global $mainframe;
$mainframe->getCfg('custom_var');